Table 1.
Summary of the datasets generated for simulation experiments.
| Dataset | TV Average | Cytosine Sites/Sample | Samples/Group * | Cut-Point | Accuracy | Sen. | Spe. | FDR |
|---|---|---|---|---|---|---|---|---|
| 1. Model building & cross-validation | 0.0356 | 1,000,000 | 3 | 0.3500 | 1.0000 | 1.0000 | 1.0000 | 0.0000 |
| 2. Model building & cross-validation | 0.1332 | 1,000,000 | 3 | 0.9404 | 0.9998 | 0.9997 | 1.0000 | 0.0000 |
| 3. Model building & cross-validation | 0.1845 | 1,000,000 | 3 | 0.9251 | 1.0000 | 1.0000 | 1.0000 | 0.0000 |
| 4. External data for validation | 0.0356 | 1,000,000 | 50 | 0.3500 | 1.0000 | 1.0000 | 1.0000 | 0.0000 |
| 5. External data for validation | 0.1332 | 1,000,000 | 50 | 0.9404 | 0.9998 | 1.0000 | 1.0000 | 0.0000 |
| 6. External data for validation | 0.1845 | 1,000,000 | 50 | 0.9251 | 1.0000 | 0.9999 | 1.0000 | 0.0000 |
| 7. Model building & cross-validation | 0.0356 | 1,000,000 | 50 | 0.3500 | 1.0000 | 1.0000 | 1.0000 | 0.0000 |
| 8. Model building & cross-validation | 0.1332 | 1,000,000 | 50 | 0.8667 | 1.0000 | 1.0000 | 1.0000 | 0.0000 |
| 9. Model building & cross-validation | 0.1845 | 1,000,000 | 50 | 0.8306 | 1.0000 | 1.0000 | 1.0000 | 0.0000 |
| 10. External data for validation | 0.0356 | 1,000,000 | 50 | 0.3500 | 1.0000 | 1.0000 | 1.0000 | 0.0000 |
| 11. External data for validation | 0.1332 | 1,000,000 | 50 | 0.8667 | 1.0000 | 1.0000 | 1.0000 | 0.0000 |
| 12. External data for validation | 0.1845 | 1,000,000 | 50 | 0.8306 | 1.0000 | 1.0000 | 1.0000 | 0.0000 |
* Four independent control samples were used to build the reference sample (the centroid) for each simulation 1 to 6; while twenty were used for simulations 7 to 12. All the R scripts for these simulations are available at https://git.psu.edu/genomath/MethylIT_examples.